PASEXP_IPA: PASEXP_IPA, calculate relative expression of IPA regions

In RJWANGbioinfo/APAlyzer: A toolkit for APA analysis using RNA-seq data

PASEXP_IPA, calculate relative expression of IPA regions

Description

Map reads to IPA regions and calculte relative expression of aUTR and cUTR regions.

Usage

    PASEXP_IPA(dfIPAraw, dfLEraw, flS, Strandtype="NONE", nts=1, minMQS=0, SeqType = "SingleEnd")

Arguments

dfIPAraw	a dataframe containing 8 colmuns for Intronic PASs: 'PASid', 'gene_symbol', 'Chrom', 'Strand', 'Pos', 'upstreamSS', 'downstreamSS'. 'upstreamSS' means closest 5'/3' splice site to IPA, 'downstreamSS' means closest 3' splice site
dfLEraw	a dataframe containing 5 colmuns for 3' least exon: 'gene_symbol', 'Chrom', 'Strand', 'LEstart', 'TES'. 'LEstart' means the start position of last 3' exon.
flS	bamfile lists containing the file and path of bam files
Strandtype	strand type of the bam file; "forward" is forwand sequencing, "invert" is reverse sequencing and "NONE" is non-strand specific, Default is "NONE".
nts	number of threads used for computing, parameter used by featureCounts, nthread option, Default is 1
minMQS	minimum mapping quality score of counted reads, parameter used by featureCounts, minMQS option, Default is 0
SeqType	set the sequencing type of reads in bam files can be either 'SingleEnd' (default) or 'ThreeMostPairEnd'.

Value

The function PASEXP_IPA() return a dataframe containning reads count, RPKM and relative expression of aUTR and cUTR for each gene

Author(s)

Ruijia Wang

Examples

## count reads mapped to IPA regions and
## calculte relative expression of aUTR and cUTR regions
## using forward sequencing
    library("TBX20BamSubset")
    library("Rsamtools")
    library("GenomicAlignments")
	library("repmis")
    flsall = getBamFileList()
	URL="https://github.com/RJWANGbioinfo/PAS_reference_RData/blob/master/"
	file="mm9_REF.RData"
	source_data(paste0(URL,file,"?raw=True"))
    IPA_OUTraw=PASEXP_IPA(dfIPA, dfLE, flsall, Strandtype="forward", nts=1)

RJWANGbioinfo/APAlyzer documentation built on Dec. 6, 2024, 3:36 p.m.